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193 results for “trait analysis”
Data from: On the link between functional traits and growth rate: meta-analysis shows effects change with plant size, as predicted
A plant's growth rate is seen as a central element of its ecological strategy, and as determined by its traits.Yet the literature is inconsistent about the empirical correlation between functional traits and growth, casting doubt on the capacity of some prominent traits to influence growth rate. We propose that traits should influence growth in a way that depends on the size of individual plants. We outline mechanisms and hypotheses based on new theoretical work, and test these predictions in tree species using a meta-analysis of 103 studies (> 500 correlations) for five traits (specific leaf area, wood density, maximum height, seed mass and maximum assimilation rate).We also recorded data for 14 other traits commonly used in the trait literature.To capture the effects of plant size, we tested for a shift in the direction of correlation between growth rates and each trait across three ontogenetic stages: seedling,sapling and adult. Results were consistent with predictions, although there were some limitations arising from unequal numbers of observation across ontogenetic stages.Specific leaf area was correlated with relative growth rate in seedlings but not in adult plants.Correlations of growth with wood density were not affected by ontogenetic stage. Seed mass, assimilation rate and maximum height were correlated with relative growth rate only in one ontogenetic stage category: seedlings,seedlings and adults,respectively. Although we were able to confirm several of our theoretical predictions,major knowledge gaps still exist in the trait literature.For example,for one third of the traits considered,the majority (> 75%) of reported correlations with growth came from the same ontogenetic stage. Synthesis: We show for some traits, how trait-growth correlations change in a predictable way with plant size.Our understanding of plant strategies should shift away from describing species as having a fixed growth strategy throughout their life (on a continuous axis from slow to fast growth), in favour of a size-dependent growth trajectories.
Data from: A phylogenetic analysis of trait convergence in the spring flora
In temperate deciduous forests, spring flowering plants exhibit remarkable similarity in a number of characteristics, including reproductive, vegetative, and ecological traits. The apparent convergence of floral traits, especially corolla colour, among spring flowering species has been well documented, but remains poorly understood. Here we review adaptive hypotheses and predictions that have been proposed to explain the apparent correlation between spring flowering and a suite of traits. We investigated the correlation between flowering phenology (i.e., spring or nonspring) and several key traits using phylogenetic comparative methods. Through this analysis we were able to confirm the existence of a correlation for five of the six traits examined. Specifically, spring flowering is shown to have evolved in a correlated fashion with reproductive schedule (perennial vs. annual), light corolla colour, fruit type, growth form, and forest strata layer. In general, our survey determined that spring flowering species are perennial, have light coloured corollas, a herbaceous growth form, and tend to occupy the understory of the forest. These results are discussed in light of the reviewed adaptive hypotheses and the spring pollination environment.
Data from: Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis
We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence, and mutation rates. We study, by means of a mathematical model and bifurcation analysis, conditions under which the wild-type and mutant viruses, which compete for the same host cells, can coexist. The coexistence conditions are formulated in terms of the basic reproductive numbers of the strains, a maximum value of the mutation rate, and the virulence of the pathogens. The analysis reveals that parameter space can be divided into five regions, each with distinct dynamics, that are organised around degenerate Bogdanov-Takens and zero-Hopf bifurcations, the latter of which gives rise to a curve of transcritical bifurcations of periodic orbits. These results provide new insights into the conditions by which viral populations may contain multiple coexisting strains in a stable manner.
Data from: Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens
Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r2greater than or equal to0.3) in both traditional and village chickens at pairwise marker distances of ~10 Kb; while haplotype block analysis indicates a median block size of 11–12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55–38.89 Mb) and rose comb (Gga 7:18.41–22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25–67.28 Mb, Gga 1:67.28–67.32 Mb) totalling ~75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.
Data from: Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip
Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.
Raw data associated to the paper "Analysis of species pair associations combined with functional traits reveals the effects of environmental filtering and biotic interactions in an unmanaged temperate forest"
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Supplementary material 1 from: Gruntman M, Segev U (2024) Effect of residence time on trait evolution in invasive plants: review and meta-analysis. NeoBiota 91: 99-124. https://doi.org/10.3897/neobiota.91.109251
Supplementary information
Rapid evolution of life history traits in response to warming, predation and competition: a meta-analysis
<p>Although studies quantifying evolutionary change in response to the selective pressures that organisms face in the wild have demonstrated that organisms <i>can</i> evolve rapidly, we lack a systematic assessment of the frequency, magnitude and direction of rapid evolutionary change across taxa. To address this gap, we conducted a meta-analysis of 58 studies that document the effects of warming, predation or competition on the evolution of body size, development rate or fecundity in natural or experimental animal populations. We tested whether there was a consistent effect of any selective agent on any trait, whether the direction of these effects align with theoretical predictions, and whether the three agents select in opposing directions on any trait. Overall, we found weak effects of all three selective agents on trait evolution: none of our nine trait by selective agent combinations had an overall effect that differed from zero, only 31% of studies had a significant within-study effect, and attributes of the included studies generally did not account for between-study variation in results. One notable exception was that predation targeting adults consistently resulted in the evolutoin of smaller prey body size. We discuss potential causes of these generally weak responses and consider how our results inform the ongoing development of eco-evolutionary research.</p>
Diversification of Crassula: Phylogenetic analysis and life-form traits
<p>These datasets are associated with the published paper - "Evidence linking life form to a major shift in diversification rate in <em>Crassula</em>" (DOI:10.1002/ajb2.1797) </p> <p><i>Crassula</i> L. (Crassulaceae) is a characteristic element of the southern African flora, occurring in a wide range of habitats, and it exhibits a remarkable diversity of life forms. However, whether any particular life-form trait has shaped species diversification in <em>Crassula </em>has remained unexplored. Our study aimed to investigate diversification patterns within Crassula and identify potential links to its life-form evolution. A phylogenetic tree of 140 <em>Crassula </em>taxa was reconstructed using plastid and nuclear loci, and dated based on the nuclear DNA information only. We reconstructed ancestral life-form characters to estimate the evolutionary trends of ecophysiological change, and subsequently estimated net diversification rates. The datasets presented here summarise the life-form classification (incl. life-history strategies and growth forms) of all <em>Crassula </em>species and the data from our phylogenetic analysis.</p>
Data from: A longitudinal analysis of the growth rate and mass of tail feathers in a great tit population: ontogeny, genetic effects and relationship between traits
<p class="MsoNoSpacing">Feathers have a diversity of functions in birds and are costly to produce, so their growth rate and mass can be reliable indicators of nutritional condition at the time of production. Despite the potential for feather metrics to advance our understanding of foraging, they are underused in avian ecology. One reason for this is the difficulty of interpreting whether individual variation is driven by ontogenetic, genetic, or environmental effects, which is exacerbated by the fact that most analyses have been done on cross-sectional data. We addressed this deficit using a longitudinal dataset of tail feathers collected from Great tits <em>Parus major</em> to test for ontogenetic and genetic effects on growth rate, mass and length, while controlling for body/feather size differences and other confounding factors. First, we found that the type of moult episode and experimentally-induced replacement differentially affected the length, mass and growth of feathers, providing evidence of an ontogenetic effect that should be considered when comparing these feather traits across individuals as a measure of condition. Second, we detected moderate to high repeatability and heritability values from parent-offspring regression for these three feather traits, which are suggestive of an underlying genetic component of variation. Third, we used a mean centring within-individual approach to test whether feather growth rate and feather mass (length-corrected) are indeed positively correlated with each other as overlapping indicators of body condition in birds, and found that this association, although positive, is weak and only significant between individuals. This suggests that both metrics are not so intimately linked as originally thought, and probably have different sensitivities to variation in foraging performance and ecological conditions. Together with the higher plasticity of feather growth rate compared to feather mass, our results support the idea that feather growth rate is better suited for examining short-term responses to environmental variation.</p>
Comparative analysis of passerine feather traits: data and script
<p></p> <p class="Normln1"><span>Tropical bird species are characterised by a comparatively slow pace of life, being predictably different from their temperate zone counterparts in their investments in growth, survival and reproduction. In birds, <span>the development of functional plumage is often considered energetically demanding investment, with consequences on individual fitness and survival. However, </span>current knowledge of interspecific variation in feather growth patterns is mostly based on species of the northern temperate zone. We<span> evaluated patterns in tail feather growth rates (FGR) and feather quality (</span>stress-induced <span>fault bar occurrence; FBO), </span>using<span> </span>1518 individuals of 167 species and 39 passerine families inhabiting Afrotropical and northern temperate zones. We <span>detected</span> a clear difference in feather traits between species breeding in the temperate and tropical zones, with the latter having significantly slower FGR and three times higher FBO. Moreover, trans-Saharan latitudinal migrants resembled temperate zone residents in that they exhibited a comparatively fast FGR and low FBO, despite sharing moulting environments with tropical species. Our results reveal convergent latitudinal shifts in feather growth investments (latitudinal syndrome) across unrelated passerine families and underscore the importance of breeding latitude in determining cross-species variation in key avian life-history traits.</span></p>
Supplemental R code and csv files for statistical analysis on Doi et al. "Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities"
<p>Supplemental R code and csv files for statistical analysis on Doi et al. "Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities"</p>
Effects of blood cell traits on cardiovascular morpho-functional phenotypes: Evidence from Mendelian randomization analysis
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FIGURE 1 in Taxonomic Studies Using Multivariate Analysis of Eriobotrya Based on Morphological Traits
FIGURE 1. UPGMA dendrogram of Eriobotrya species and its related genera.
Big Five Personality Traits and Online Learning: A Meta-analysis of 40 Years' Research
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Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa
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Data from: Influence of a growth hormone transgene on the genetic architecture of growth-related traits: a comparative analysis between transgenic and wild-type coho salmon
Genetic engineering has been increasingly applied to many commercially important plant and animal species, generating phenotypic changes that are not observed in natural populations and creating genetic interactions that have not experienced natural selection. The degree to and way in which such human-induced genetic variation interacts with the rest of the genome is currently largely unknown. Integrating such information into ecological and risk assessment frameworks is crucial to understand the potential effects of genetically modified organisms in natural environments. Here, we performed QTL mapping to investigate the genetic architecture of growth-related traits in non-transgenic (NT) and growth hormone transgenic (T) coho salmon with large changes in growth and related physiology, with the aim of identifying how an inserted transgene might influence the opportunity for selection. These fish shared the same parental genetic background, thus allowing us to determine whether the same or different loci influence these traits within the two groups. The use of over 1700 loci, derived from Restriction site Associated DNA Sequencing, revealed that different genomic regions were linked with growth over time between the two groups. Additionally, the effect sizes of detected QTL appear to have been influenced by the transgene. Direct comparison of QTL between the T and NT fish during two size-matched periods identified little overlap in their location. Taken together, the results showed that the transgene altered the genetic basis of growth-related traits in this species. The study has important implications for effective conservation and management of wild populations experiencing introduction of transgenes. Evolutionary changes and their ecological consequences may occur at different rates and in different directions in NT versus T individuals in response to selection. Thus assessments of phenotypic change, and hence ecological risk, should be determined periodically to evaluate whether initial estimates made with founder strains remain valid.
Data and analysis from: Two centuries of monarch butterfly collections reveal contrasting effects of range expansion and migration loss on wing traits
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Data from: Phylogenetic analysis using Lévy processes: finding jumps in the evolution of continuous traits
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Comparative analysis of passerine feather traits: data and script
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